DRAGEN
Illumina Connected Software
  • Overview
    • Illumina® DRAGEN™ Secondary Analysis
    • DRAGEN Applications
    • Deployment Options
  • Product Guides
    • DRAGEN v4.4
      • Getting Started
      • DRAGEN Host Software
        • DRAGEN Secondary Analysis
      • Clinical Research Workflows
        • DRAGEN Heme WGS Tumor Only Pipeline
          • Quick Start
          • Sample Sheets
            • Introduction
            • Requirements
            • Templates
          • Run Planning
            • Sample Sheet Creation in BaseSpace
            • Custom Config Support
          • DRAGEN Server App
            • Getting Started
            • Launching Analysis
            • Command Line Options
            • Output
            • Advanced Topics
              • Custom Workflow
              • Custom Config Support
              • Illumina Connected Insights
          • ICA Cloud App
            • Getting Started
            • Launching Analysis
            • Advanced Topics
              • Custom Workflow
              • Custom Config Support
              • Post Processing
              • Illumina Connected Insights
          • Analysis Output
          • Analysis Methods
          • Troubleshooting
        • DRAGEN Solid WGS Tumor Normal Pipeline
          • Quick Start
          • Sample Sheets
            • Introduction
            • Requirements
            • Templates
          • Run Planning
            • Sample Sheet Creation in BaseSpace
            • Custom Config Support
          • DRAGEN Server App
            • Quick Start
            • Getting Started
            • Launching Analysis
            • Command Line Options
            • Output
            • Advanced Topics
            • Custom Workflow
              • Custom Config Support
            • Illumina Connected Insights
          • ICA Cloud App
            • Getting Started
            • Launching Analysis
            • Output
            • Advanced Topics
              • Custom Workflow
              • Custom Config Support
              • Post Processing
              • Illumina Connected Insights
          • Analysis Output
          • Analysis Methods
          • Troubleshooting
      • DRAGEN Recipes
        • DNA Germline Panel UMI
        • DNA Germline Panel
        • DNA Germline WES UMI
        • DNA Germline WES
        • DNA Germline WGS UMI
        • DNA Germline WGS
        • DNA Somatic Tumor-Normal Solid Panel UMI
        • DNA Somatic Tumor-Normal Solid Panel
        • DNA Somatic Tumor-Normal Solid WES UMI
        • DNA Somatic Tumor-Normal Solid WES
        • DNA Somatic Tumor-Normal Solid WGS UMI
        • DNA Somatic Tumor-Normal Solid WGS
        • DNA Somatic Tumor-Only Heme WGS
        • DNA Somatic Tumor-Only Solid Panel UMI
        • DNA Somatic Tumor-Only Solid Panel
        • DNA Somatic Tumor-Only Solid WES UMI
        • DNA Somatic Tumor-Only Solid WES
        • DNA Somatic Tumor-Only Solid WGS UMI
        • DNA Somatic Tumor-Only Solid WGS
        • DNA Somatic Tumor-Only ctDNA Panel UMI
        • Illumina scRNA
        • Other scRNA prep
        • RNA Panel
        • RNA WTS
      • DRAGEN Reference Support
        • Prepare a Reference Genome
      • DRAGEN DNA Pipeline
        • DNA Mapping
        • Read Trimming
        • DRAGEN FASTQC
        • Sorting and Duplicate Marking
        • Small Variant Calling
          • ROH Caller
          • B-Allele Frequency Output
          • Somatic Mode
          • Pedigree Analysis
          • De Novo Small Variant Filtering
          • Autogenerated MD5SUM for VCF Files
          • Force Genotyping
          • Machine Learning for Variant Calling
          • Evidence BAM
          • Mosaic Detection
          • VCF Imputation
          • Multi-Region Joint Detection
        • Copy Number Variant Calling
          • Available pipelines
            • Germline CNV Calling (WGS/WES)
            • Germline CNV Calling ASCN (WGS)
            • Multisample Germline CNV Calling
            • Somatic CNV Calling ASCN (WGS)
            • Somatic CNV Calling WES
            • Somatic CNV Calling ASCN (WES)
          • Additional documentation
            • CNV Input
            • CNV Preprocessing
            • CNV Segmentation
            • CNV Output
            • CNV ASCN module
            • CNV with SV Support
            • Cytogenetics Modality
        • Repeat Expansion Detection
          • De Novo Repeat Expansion Detection
        • Targeted Caller
          • CYPDB6 Caller
          • CYP2D6 Caller
          • CYP21A2 Caller
          • GBA Caller
          • HBA Caller
          • LPA Caller
          • Rh Caller
          • SMN Caller
        • Structural Variant Calling
          • Structural Variant De Novo Quality Scoring
          • Structural Variant IGV Tutorial
        • VNTR Calling
        • Population Genotyping
        • Filter Duplicate Variants
        • Ploidy Calling
          • Ploidy Estimator
          • Ploidy Caller
        • Multi Caller
        • QC Metrics Reporting
        • JSON Metrics Reporting
        • HLA Typing
        • Biomarkers
          • Tumor Mutational Burden
          • Microsatellite Instability
          • Homologous Recombination Deficiency
          • BRCA Large Genomic Rearrangment
          • DRAGEN Fragmentomics
        • Downsampling
          • Fractional (Raw Reads) Downsampling
        • Unique Molecular Identifiers
        • Indel Re-aligner (Beta)
        • Star Allele Caller
        • High Coverage Analysis
        • CheckFingerprint
        • Population Haplotyping (Beta)
        • DUX4 Rearrangement Caller
      • DRAGEN RNA Pipeline
        • RNA Alignment
        • Gene Fusion Detection
        • Gene Expression Quantification
        • RNA Variant Calling
        • Splice Variant Caller
      • DRAGEN Single Cell Pipeline
        • Illumina PIPseq scRNA
        • Other scRNA Prep
        • scATAC
        • Single-Cell Multiomics
      • DRAGEN Methylation Pipeline
      • DRAGEN MRD Pipeline
      • DRAGEN Amplicon Pipeline
      • Explify Analysis Pipeline
        • Kmer Classifier
        • Kmer Classifier Database Builder
      • BCL conversion
      • Illumina Connected Annotations
      • ORA Compression
      • Command Line Options
        • Docker Requirements
      • DRAGEN Reports
      • Tools and Utilities
    • DRAGEN v4.3
      • Getting Started
      • DRAGEN Host Software
        • DRAGEN Secondary Analysis
      • DRAGEN Reference Support
        • Prepare a Reference Genome
      • DRAGEN DNA Pipeline
        • DNA Mapping
        • Read Trimming
        • DRAGEN FASTQC
        • Sorting and Duplicate Marking
        • Small Variant Calling
          • ROH Caller
          • B-Allele Frequency Output
          • Somatic Mode
          • Joint Analysis
          • De Novo Small Variant Filtering
          • Autogenerated MD5SUM for VCF Files
          • Force Genotyping
          • Machine Learning for Variant Calling
          • Evidence BAM
          • Mosaic Detection
          • VCF Imputation
          • Multi-Region Joint Detection
        • Copy Number Variant Calling
          • CNV Output
          • CNV with SV Support
          • Multisample CNV Calling
          • Somatic CNV Calling WGS
          • Somatic CNV Calling WES
          • Allele Specific CNV for Somatic WES CNV
        • Repeat Expansion Detection
          • De Novo Repeat Expansion Detection
        • Targeted Caller
          • CYPDB6 Caller
          • CYP2D6 Caller
          • CYP21A2 Caller
          • GBA Caller
          • HBA Caller
          • LPA Caller
          • Rh Caller
          • SMN Caller
        • Structural Variant Calling
          • Structural Variant De Novo Quality Scoring
        • VNTR Calling
        • Filter Duplicate Variants
        • Ploidy Calling
          • Ploidy Estimator
          • Ploidy Caller
        • Multi Caller
        • QC Metrics Reporting
        • HLA Typing
        • Biomarkers
          • Tumor Mutational Burden
          • Microsatellite Instability
          • Homologous Recombination Deficiency
          • BRCA Large Genomic Rearrangment
          • DRAGEN Fragmentomics
        • Downsampling
          • Fractional (Raw Reads) Downsampling
          • Effective Coverage Downsampling
        • Unique Molecular Identifiers
        • Indel Re-aligner (Beta)
        • Star Allele Caller
        • High Coverage Analysis
        • CheckFingerprint
        • Population Haplotyping (Beta)
        • DUX4 Rearrangement Caller
      • DRAGEN RNA Pipeline
        • RNA Alignment
        • Gene Fusion Detection
        • Gene Expression Quantification
        • RNA Variant Calling
        • Splice Variant Caller
      • DRAGEN Single-Cell Pipeline
        • scRNA
        • scATAC
        • Single-Cell Multiomics
      • DRAGEN Methylation Pipeline
      • DRAGEN Amplicon Pipeline
      • Explify Analysis Pipeline
        • Kmer Classifier
        • Kmer Classifier Database Builder
      • DRAGEN Recipes
        • DNA Germline Panel UMI
        • DNA Germline Panel
        • DNA Germline WES UMI
        • DNA Germline WES
        • DNA Germline WGS UMI
        • DNA Germline WGS
        • DNA Somatic Tumor-Normal Solid Panel UMI
        • DNA Somatic Tumor-Normal Solid Panel
        • DNA Somatic Tumor-Normal Solid WES UMI
        • DNA Somatic Tumor-Normal Solid WES
        • DNA Somatic Tumor-Normal Solid WGS UMI
        • DNA Somatic Tumor-Normal Solid WGS
        • DNA Somatic Tumor-Only Heme WGS
        • DNA Somatic Tumor-Only Solid Panel UMI
        • DNA Somatic Tumor-Only Solid Panel
        • DNA Somatic Tumor-Only Solid WES UMI
        • DNA Somatic Tumor-Only Solid WES
        • DNA Somatic Tumor-Only Solid WGS UMI
        • DNA Somatic Tumor-Only Solid WGS
        • DNA Somatic Tumor-Only ctDNA Panel UMI
        • RNA Panel
        • RNA WTS
      • BCL conversion
      • Illumina Connected Annotations
      • ORA Compression
      • Command Line Options
      • DRAGEN Reports
      • Tools and Utilities
  • Reference
    • DRAGEN Server
    • DRAGEN Multi-Cloud
      • DRAGEN on AWS
      • DRAGEN on AWS Batch
      • DRAGEN on Microsoft Azure
        • Run DRAGEN VM on Azure
      • DRAGEN on Microsoft Azure Batch
        • Azure Batch Run Modes
    • DRAGEN Licensing
      • DRAGEN Server Licensing
      • DRAGEN Cloud Licensing
    • DRAGEN Application Manager
    • Support
    • Resource Files
      • Noise Baselines
    • Supplementary Information
    • Troubleshooting
    • Citing DRAGEN software
    • Release Notes
    • Revision History
Powered by GitBook
On this page
  • Command-Line Options
  • Example to generate panel of normal
  • Example command lines
  • LR Output

Was this helpful?

Export as PDF
  1. Product Guides
  2. DRAGEN v4.4
  3. DRAGEN DNA Pipeline
  4. Biomarkers

BRCA Large Genomic Rearrangment

Large genomic rearrangements affecting one or more exons account for approximately 5~10% of all disease-causing mutations in BRCA1 and BRCA2 genes in patients with hereditary breast and ovarian cancer syndrome. DRAGEN LR can detect within gene large genomic rearrangements in tumor-only mode for targeted panels such as TruSight Oncology 500. The performance has been verified for BRCA1/2 with TruSight Oncology 500 Assay.

Command-Line Options

Use the following command-line options to run large rearrangement detection. The same cmd line options can be tested on other tumor-only pipelines.

--tso500-solid-brca-lr=true Set to true enable large rearrangement parameters. This is not limited to TruSight Oncology 500 Assay.

--cnv-normals-list Specify the panel of normal samples to measure instrinsic biases of the upstream processes to allow for proper normalization. To generate a panel of normals, see the example command line. The panel of normal samples should be well matched to the case sample under analysis.

--cnv-target-bed Specify the targeted regions of the panel.

--cnv-within-gene-lr-bed Specify the gene regions in BED format to do large rearrangment calling. Example file:

chr17	41196312	41277500	BRCA1
chr13	32889617	32973809	BRCA2

Example to generate panel of normal

Run the following command on each normal sample to generate .target.counts.gc-corrected.gz file.

dragen \
-r <HASHTABLE> \
--output-directory <OUTPUT> \
--output-file-prefix <SAMPLE> \
--enable-cnv true \
--cnv-enable-gcbias-correction true \
--cnv-enable-split-intervals true \
--cnv-target-bed <BED> \
--tumor-bam-input <BAM>

Put the path to the generated .target.counts.gc-corrected.gz files into a txt file. One file per line. This will be the file given to --cnv-normals-list.

Example command lines

dragen \
-r <HASHTABLE> \
--output-directory <OUTPUT> \
--output-file-prefix <SAMPLE> \
--tso500-solid-brca-lr true \
--cnv-normals-list <PON> \
--cnv-target-bed <BED> \
--cnv-within-gene-lr-bed <GENE.bed> \
--tumor-bam-input <BAM>

LR Output

The output file .cnv.LR.json contains the breakpoints detected for each specified gene region. The following is an example output file.

"Breakpoints": {
        "BRCA1": {
            "nSegs": "1",
            "segments": [
                {
                    "id": "BRCA1.1",
                    "chromosome": "chr17",
                    "start": "41197309",
                    "stop": "41276383",
                    "nBin": "95",
                    "segmentMean": "0.77611423479585684",
                    "segmentMeanLog2": "-0.36565907927374325"
                }
            ]
        },
         "BRCA2": {
            "nSegs": "3",
            "segments": [
                {
                    "id": "BRCA2.1",
                    "chromosome": "chr13",
                    "start": "32890596",
                    "stop": "32945239",
                    "nBin": "61",
                    "segmentMean": "0.80852624347115876",
                    "segmentMeanLog2": "-0.3066334928504777"
                },
                {
                    "id": "BRCA2.2",
                    "chromosome": "chr13",
                    "start": "32950805",
                    "stop": "32954284",
                    "nBin": "8",
                    "segmentMean": "0.45378940514841132",
                    "segmentMeanLog2": "-1.1399051688173489"
                },
                {
                    "id": "BRCA2.3",
                    "chromosome": "chr13",
                    "start": "32956413",
                    "stop": "32972909",
                    "nBin": "10",
                    "segmentMean": "0.890907164346186",
                    "segmentMeanLog2": "-0.16665298919550192"
                }
            ]
        }
    }

Note that coordinate follows BED format [start,stop) suggesting:

  • start: segment starting coordinate. (0-base inclusive: first base on the chromosome is numbered 0. start coordinate is included in the interval)

  • stop: segment stop coordinate. (0-base exclusive: first base on the chromosome is numbered 0. stop coordinate is not included in the interval)

PreviousHomologous Recombination DeficiencyNextDRAGEN Fragmentomics

Last updated 2 days ago

Was this helpful?